Pokémon: Red
by jacoman52
Summary: The original Pokémon journey like never experienced before. In 1998, a kid from Earth takes his first steps into the Pokémon World. There, as he rises to the challenge of the Indigo Plateau, he must unravel the mystery behind an ancient civilization uniting the multiverse and confront a sinister organization whose tampering with time and space threatens the very fabric of reality.
1. Prologue: The Road to Honshū

**Prologue: The Path to Honshū**

* * *

 _Earth, United States of America, Universe Prime, 1998_

* * *

Gzl;a gjadvao;djk; !

I smacked the keyboard with my fists, and my command prompt window sputtered gibberish in protest. I was about to slap this computer into next week.

Eighteen hours creeping down the dark backwoods of the Internet, and nobody—I mean nobody—had heard of 008-03-607.

All of this started three weeks ago, when my best friend Brent found a flat, origami swallow wedged in his binder at school. When he unfolded it, the paper showed a pencil-drawn picture of a butterfly.

If Brent were any ordinary kid, he would have thought maybe some girl was trying to flirt with him. He had a lot of that problem, and I had exactly none of it.

But Brent noticed two things about the picture. First, it was way too good to have been drawn by a kid. We're talking professional insect-sketching—if there was such a thing. Second, on the butterfly's right wing was a symbol of three interlocking circles, half-covered with spikes. He had seen it before. So had I.

"Jason. You need to come over. Now," Brent called me after he got home that day, "I got some kind of crypto-picture from _them_."

"What? How?" I asked. I had just popped open some frozen bagel bites, and wasn't too keen on letting them go to waste.

"They must've slipped it into my backpack. It's got their symbol, and I think there's a message in it."

I looked forlornly at my bagel bites rotating in the warm yellow glow of the microwave. How did Suite 3 get into our school? One of the teachers? A janitor? Maybe a kid's parent worked for them and told their kid to slip Brent the note.

"Give me food?" I sighed.

"I bring offerings of beef jerky and those little mini Hot Pockets."

"Regular, or those weird breakfast ones?"

"Both. Blended together into the greatest monstrosity you've ever—"

"See you in fifteen."

Our 90s weren't like most kids' 90s. I had a colorful history with, shall we say, off-the-radar organizations? Yeah, off-the-radar is good. Apparently genius kids with a knack for codes and pattern analysis were a commodity for some shady groups even back when the internet was just starting to get big.

When I was nine, I was lucky—blessed, really—to stumble across some of the good guys. Suite 3, the team with the spiky rings? They were not the good guys.

My parents didn't know my secret, and maybe never would. Brent had found out a year later, and for the last six months he had been helping me with a project called Avalon, which—well, I'll get to that later.

Anyway, sometimes things like this got dropped into our laps. It was better, safer, not to ignore them.

"Got it!" Brent said after five hours of combing through websites showing every kind of moth and butterfly you can imagine. I scarfed down a last bite of cheesy, tomato-y goodness and hopped over to peer over Brent's shoulder.

"It's a Great Purple Emperor butterfly," he said "They live in Asia."

The website showed dozens of photos of the butterfly—black-tipped wings, daisy yellow spots, and a beautiful, plum and navy sheen.

"Click on that one," I said.

When Brent zoomed in, it was a photo of the same butterfly that was in the drawing. I mean the _exact_ same one. The only difference was, it was missing the three ring symbol. And a few dots, too. The picture had a watermark with a picture of a wheat stalk and the letters FAO.

"FAO?" I asked.

With a few keystrokes, Brent pulled up a page.

"Food and Agriculture Organization. United Nations."

"What is the UN doing with Suite Number 3?"

"They're probably not. SN-3 could have hacked the image to remove those pixels."

"Or someone else could have. Who took the picture?"

More typing.

"Doesn't say. I mean, there is, like, zero trail. Somebody doesn't want to be found."

"Or at least somebody doesn't want to be found easily."

But we did find him. Sort of. After three days of poking around sketchy forums, I got a message from an untraceable private server:

 _I hear you've been dieing to catch some insects. These are some of my favorites._

 _—The Entomologist_

Entomologist. A bug scientist. Cute. Attached were three more pictures of insects: a preying mantis, a beetle, and a moth.

What. The. Heck. And how do you misspell "dying"? Either these people were geniuses in cryptology but didn't pass their spelling tests, or . . . or was the misspelling part of another code?

I could basically write a whole book on what it took to figure everything out—this guy was good—, but I'll give you the Reader's Digest version.

Brent guessed that the numbers for the missing pixels on the first butterfly photo were part of a code-breaking cipher. There was also a paper re-published by the FAO on the same day that Brent got the picture. The paper, weirdly enough, was about "aquatic insects of the Sukomo River" near a city in Japan called Hakone, which was odd because the paper had been written seven years ago. When you looked into the paper's source code, there was a place to use the butterfly photo's cipher.

We cracked the code, and almost all the numbers adjusted to become map coordinates for cities in Japan: Yokohama, Taeyama, Sakura, Tsuchiura, and a few others.

One city showed up twice: Machida—the same town the "aquatic insects" paper was published in. We figured that was important.

Another place that didn't appear on the pixel code was Fujiyoshida, a plateau town near Mt. Fuji—swanky lakeside hotels, nice views, that sort of thing. Its location was hidden in a code in the Sukomo River article itself. We added the town to our growing list of clues.

That's when things started getting a little nuts. I started getting anonymous inbox messages. Some were warnings, and some were from people trying to find out who we were.

 _What you're doing is dangerous_ , said one email, _Entomology has consequences. I told him that._

Somebody else apparently thought I was part of their secret society or whatever, because they sent me a message that made absolutely no sense, but it was obviously addressed to someone who could understand it:

 _Confirmed. September 1, 1923, Oshima, result of sub-spatial tampering. Now facing WK event?_

Oshima was an island off Japan's main island, and one of the locations on the list. When I tried to bluff a response to find out what a WK event was, I didn't get a reply.

I eventually found the original preying mantis picture online. Shortly after that, Brent found the beetle and the moth. We used the pixel code on any changes between the real pictures and the Entomologist's pictures, and we came up with a string of numbers. These numbers weren't map coordinates; they turned out to be a complicated mathematical code that took two weeks for me to solve. It coughed up a single number sequence: 008-03-607.

So here I was, three days and six boxes of bagel bites later, trying to figure out what the heck that meant. We had tried everything: product serial numbers; network connections; museum archives; talking to hacker groups. We even searched through some old vacuum cleaner sales records. I shut my computer down and tried to let my brain take a break. Sometimes that helped me figure out a problem faster.

The next day, it hit me. My class was on our weekly trip to the school library, and I was browsing through the Animorphs stories—most of which I'd already read—when I started thinking: _books_.

Chapter books? No, that would be silly. Science books on insects?

I looked down at the book in my hand. _The Solution_ , the newest in the series.

That was it.

That afternoon, I practically kicked down Brent's front door. "How many of those towns in Japan have colleges in them?"

"Uh, do you knock?"

"Hurry up! I think I figured it out!"

"Okay, dad. Hold your friggin hors— Well, a lot of them do."

"Can we look up the books and other stuff they put out?"

"I can hack their libraries' electronic catalogs, yeah."

That's how we found 008-03. It was the volume and issue number of a big-time journal.

The final clue was in the Entomologist's message: the way he had spelled "dying" wrong.

It turns out, there was a Journal of Differential and Integral Equations (DIE), and a short paper in Volume 8, Issue 3 was written by someone at the Tokyo Institute of Technology. It was a paper published three years ago, and it started on page 607.

"Nailed it," said Brent, "And, whoa. This is not about bugs."

I leaned in closer. "Oh, great. It's a bunch of math."

"Not just any math," Brent popped a couple mini Hot Pockets in his mouth, "Differential and Integral Equations."

Differential and Integral Equations, indeed. So whoever these people were, they liked calculus and things with six legs. Criminal masterminds if I'd ever known them.

Later that day, we found more Japanese colleges that might be involved by connecting the dots between professors who knew each other. Two went to high school together. Some had worked on the same research projects.

Even better, some of the papers that those professors had written held the missing designs from the emperor butterfly within their the pages. Anyone not looking for them would think they were coffee splashes or problems with the copier machine.

We found ten papers with the designs: papers on gene mutations, alternate universes, all kinds of stuff. Some of the numbers in the papers looked like they might connect to the cipher, but there was no way of knowing what order they went in.

The guy who seemed like he was at the center of it all was also the one whose paper had the dots that represented Mashido. Someone named "Satoshi T." who had written this weird article on how some universes might be more imaginary than others.

I hacked in and found his AOL username, and I sent him a simple instant message:

 _008-03-607. I'm a fan of entomology, DNA, the time-space continuum, and integral equations. Can you teach me about the emperor butterfly?_

Three days later, I got a response.

 _Kōtoku-in. October 3, 2 pm, JST (Japan Standard Time)._

 _Meet by the statue of the Great Buddha._

And that was how I began my Pokémon journey.


	2. Mysterium Tremendum et Fascinans

**Chapter 1: Mysterium Tremendum et Fascinans**

* * *

 _Earth, Japan, Island of Honshū, Kantō region, Universe Prime_

* * *

The sun broke and sparkled as I ascended in the water, light rays dancing on the surface above me like skitterbugs, golden and hungry. Two wave-tousled heads cracked through the barrier to a brain-matter sky, and we were met with the sound of jostling foam and seagulls.

I pulled off my mask and breathed in the muck and salt of Sagami Bay. It was a perfect, crisp, 70 degrees. Or 21, if you're one of those Celsius types.

"Fancy meeting you here," Brent popped up next to me, bobbing in the surf, grinning in his trademark, self-admiring way. His mask hung goofily on top of his head.

I smirked and rolled my eyes. "Yeah, you too, Einstein. Let's get to the beach. We're almost late."

The beach, Kamakura-Something-Or-Other, had more dark, coarse mud than sand, and it didn't look super tourist-y. There weren't any resorts or fancy umbrella chairs or anything—just an older couple walking slowly through the trickling waves, and a mother with a couple young kids splashing around farther down the shore. At least there were some people, so hopefully we didn't look suspicious other than the fact that we were a couple of white kids in Japan in the middle of the school year.

Oh, yeah, and we were wearing wetsuits.

We made our way up the beach where the sand quickly gave way to pavement and a beachfront neighborhood. The streets were narrow between the houses that lined the beach, and a lot of people left their garage doors open, so it was easy to find one to duck into and change.

We stripped out of our wetsuits and stuffed them into the backpacks we had brought with us. I hiked my jeans up and leaned against a bicycle while I pulled my shoes on.

The house we were in—like the others we'd passed—was tiny and made of sea-battered wood. The whole neighborhood looked like it had seen better days. Or maybe days here were always wet and overcast.

"Kinda depressing to live here," Brent said.

"Yeah . . ." I said, but in my mind, it felt wrong to agree.

I tried to look at how this would feel like home to people. It wasn't dreary, it was misty. Not weathered, but lived-in.

I had to wiggle a finger in behind my heel to get my last shoe on. I never untied them.

Brent laughed-at me, not with me-while I just about fell over myself fighting the little lip from rolling down.

"Hurry up Jason, we're going to be late."

I shot him a don't-tempt-me look as I scooped up my backpack and trotted out of the garage.

"Did you find anything out about September 1923?" I asked while we walked.

Brent popped a couple mini Hot Pockets in his mouth. Snacks were always a must when we went on these little adventures.

"Only that there was an earthquake," he said, "Pretty bad one. I still don't know what a WK event is."

The streets got busier as we got closer to Kōtoku-in, the famous temple that housed the Great Buddha. Droves of people of all shapes and colors were flocking in and out of a lively little alcove framed with natural shrubs and vines—a stark contrast to the drab gray of the pavement and the misted wooden facades of the homes and shops.

I looked at my watch. Two o'clock pm exactly.

Walking into the park was like walking through a portal to another world. We weren't at the edge of a city anymore—we were in a mystical jungle. Trees were suddenly everywhere. The sky became a ceiling of stippled green, and the silver of the clouds now peeked through like heavy light. Red and russet wood formed the shapes of little shrines and overhangs, and well-tended gravel guided the stone path that wound through the garden.

People's eyes seemed brighter here. The faces of the surrounding buildings, too, were made young again by freckles of moss and determined sprouts that found their homes in concrete cracks. Splashy, pink blossoms swayed in the breeze as twigs tapped playfully on traditionally styled rooftops.

As we rounded a bend, we saw the Great Buddha statue, a tarnished, brass behemoth from ancient times resting quietly on its pedestal. It, too, was a stark contrast to its surroundings: the people's skirts, jeans, and polos, and the snapping lenses that flashed up at the statue's form.

All of the contrasts—the light and the shade; the wood and the stone; the ancient and the modern—wove together into a picturesque scene that made me feel like I was breathing in the colors of a dozen places and times, connecting me to the essence of imagination. The murmur of the crowds, the clicking of the cameras, and the swaying of the branches made for a mesmerizing sonata, and I was a little hypnotized until I remembered why we were there.

Brent tapped me on the shoulder and nodded toward a suited man who stood alone before a pedestal that held a pot of golden flowers. He gazed upward, expressionless, at the Buddha's unreadable face.

"You think?" Brent asked.

We made our way over. The man was Japanese, older, but not elderly. I noticed sunspots on his clasped hands and kind wrinkles on his face, and his round head was balding and gray.

"I wonder if there are any purple Emperor butterflies around here," Brent said loudly enough for the man to hear.

The man didn't move at first, but I thought I saw his eyes squint a little.

I was about to signal Brent to try someone else when the man slowly turned his back to the statue. He left his hands clasped before him and locked his gaze on something distant, above the tops of the trees.

"You seek Enlightenment here?" he asked in perfect, if accented, English.

"We seek the truth," I replied.

He paused, and his eyes danced, no doubt looking for the adults that had sent us. He must be wondering why someone had sent children. How foolish and dangerous of them.

Only there were no adults. Just us. The man turned to look at the statue again. When he began to speak, I still wasn't sure if he was talking to us or to himself.

"The teachings of the Buddha were not native to Japan. Shinto came first. Our ancestors believed that every rock and tree, every blooming flower—," he touched a yellow blossom, "—Was filled with the power of its own life, its own spirit.

"Buddhism found its way here on ships and on the wind, in the way that all things come to islands. I once thought that the way of the Buddha was the only reasonable way: that all of life comes from one source. There are no elements, there is no mind. There are only manifestations of a single, divine organism to which we must return. But now . . . now I am not so sure. I have seen the spark of life in many things. In fire and water, in grass and thunder. In dragons. Are all these one, as the Buddhists say? Or are they many, as the Shinto profess? I confess I do not know."

I looked at Brent, raising an eyebrow in confusion.

"In either instance, all things have life," the man continued, "What do the European philosophers say? _Mysterium tremendum et fascinans_ —the feeling you get when you see a specially shaped stone, or a tree set apart from the others in an orchard; a flash of lightning that terrifies even as it graces the sky with its beauty; a blossom whose petals curl down farther than its sisters'. These are the spirit—or spirits—that dwell in all things. The fingerprint of God."

"Are you the Entomologist?" I pressed.

The old man raised a hand sharply.

"Not here. Now, tell me." he turned to look at us, with a glint of a smile, "Are you Shinto or Buddhist?"

I shook my head. "Neither. I'm Christian."

The man threw back his head and laughed. "Of course you are Christian. You are American! I had it all planned out—my speech. But it still applies to you, in some way, I think."

He shook his head with a surprised little smile.

"You solved it, didn't you?" he asked, "All by yourselves."

"Yes," Brent and I said softly, at the same time.

"You are children," he marveled, seeing something—or nothing—out over the trees, "Two children. He will say it was destiny."

I felt my skin tingle as though I were on the brink of a river, powerful, cool as lemon ice, beckoning me into its rush.

The man nodded like he had made up his mind.

"Come," he said, snapping us out of our trance, "My employer will be glad to meet you."

Tokyo was a sprawling gray wool that covered up the naked beauty of the countryside, but every now and then, the bare flesh of the earth poked through, raising trees and flowers into the sunlight.

Two hours after our meeting at the statue, we were deep in the city's heart, whose brick and iron chambers throbbed with the flow of tires and urgent bodies. We sat in the back of a dark-tinted car talking with the old man, who introduced himself as Yoshi Watanabe.

"I will not ask how you came here on your own," he said, "That would spoil the mystery, I think. But it is good that you are children."

Brent and I just nodded silently.

In almost every other shop we drove past, there was Pokémon merchandise on display: Pikachu, the cute little yellow mascot, was everywhere. Then there were fire-breathing lizard plushies and water-squirting turtle action figures, and a mischievous-looking cat thing turned into a Pez dispenser.

"See?" Mr. Watanabe laughed, "Spirits."

I wasn't sure what he meant by that, but it got my mind racing. Brent and I had been begging our parents to get us the Pokémon games for Christmas this year. We had seen the commercials, and it looked so cool.

I hadn't gotten to see much of the cartoon yet—just some episodes where Ash Ketchum and his friends are coming back from beating up their gym teacher or something, and then they get on this ship, and it sinks, and they get stranded on this island with giant, robot Pokémon . . . . Sorry, being a nerd over here.

Anyway, it was really cool, because you got to fight these little animals and then train them to be your pets. Some kids at our school were even bringing copies of Nintendo Power to talk about which Pokémon they wanted to catch first.

But what did little cartoon animals have to do with earthquakes, bug-collecting, and crazily complicated math problems? How did it all fit together?

We pulled into a garage while Mr. Satō entered a small, unassuming building. He returned carrying a small, silver briefcase and a knowing grin.

"Now, we must change vehicles," he said, "So our enemies won't follow us."

We ducked in and out of three more parking stations and three more cars all over the city. Two hours later, Tokyo was fading behind us, engulfed by the freedom of wilder lands—a national park, maybe. Looming at our left was Mt. Fuji, a monolith that laughed at the efforts of human hands to reach the domain of the sun and moon.

Soon, we pulled into a smaller city, nestled in the nook of a lake sparkling fire with the sunset. It was Fujiyoshida, the plateau town from the Sukomo River article code. There, a resort hotel watched quietly over the lake, with one eye toward the water and one longing up at the mountain. We pulled up to the hotel's entrance, and Mr. Satō gestured for us to step out and follow, the driver taking the rear.

We trailed through the front gardens, where the flowerbeds looked like easels dotted with fresh paint of every color, the wind brushing their pigment out onto the canvas of the water. Then we walked through an ornate lobby and took the elevator up to the highest floor.

"Looks nice enough . . . ." Brent murmured.

My heart pounded in time to the whirring of the pulleys. Each ding of the elevator felt like the next-to-last page of a story. You turn just one more page, and that's it. You're done. You find out whether the heroes save the princess or die trying.

 _Ding_.

We stepped into a corner penthouse with toasty walls and soft, warm sconces. The room was light and breezy, the autumn air streaming in through an open patio. In a scene from a feudal-era, Japanese oil painting, bamboo doors framed Mt. Fuji and the still-smoldering lake. Here, so close to the mountain, the wind's scent was crisp and full. The smells of field and forest mingled with the sweet, grassy spice of fresh-brewed tea in cups on a low-set table.

A man stepped from behind a sliding, wood panel door. He was Japanese, lanky, dressed in unassuming, relaxed-fitting garb, wore dark, round glasses, and sported short, dark hair. He didn't look much older than a teenager, honestly. His eyes were curious, like a kid's. The way he tilted his head and raised his eyebrows was puppy-like.

He spoke only Japanese in a soft, clear voice full of tenderness, "Mr. Satō? What is this?"

"These," said Mr. Satō, "Are your fellow entomologists."

The younger man's eyes widened. "Children? But . . . are they working with no one?"

Satō smiled. "I thought it was appropriate. They look to be the same age as the children in the story."

Brent and I asked each other a silent question: What story?

The young man's mouth hung open for a moment, apparently too stunned for words. Then, he shuffled over to us quickly, like he had forgotten his manners.

"Of course!" he bowed, "Welcome, welcome! Please, sit!"

The driver stepped outside to keep watch, and the four of us knelt on pads at the table for tea.

"I am Satoshi," the man began, "As you may have guessed, I am the Entomologist. Forgive me, your age should not surprise me. Does not surprise me. I know what people of any age can do. You are no different from the rest of us."

I was instantly drawn to this man. His kindness; his passion; his ideals . . . he was everything I wanted to become.

"We have so many questions," Brent said as Satō translated for us, "Are you with SN-3?"

Satoshi frowned, "No, I don't know an SN-3. Numerous hacker groups have gotten wind of our research, but I don't think they fully realize the situation we are in. You were the first to put the pieces together, as far as we know. To connect the science to our organization."

"The Integral and Differential equations article," I said, "And the research on genetics, evolution, and alternate universes."

"And the earthquake," Brent added.

We were trying not to show how little we knew so he would keep talking and let something slip. Basic spy stuff.

"Yes, precisely," said Satoshi, "I sometimes dapple in scientific studies, but I had much to learn, of course. And we had to find people to help us make the bridge a reality. I'm a game designer," he laughed, "Not a physicist."

A game designer. Not a physicist. I wracked my brain, trying to find the connections.

"You don't work for the government," I said.

"Oh, no, no," Satoshi laughed again, "We're a small company. We just happened to stumble across something big. It all came together. You see, I really did love collecting insects in my childhood. And we thought the game could be really fun and exciting. A chance to fall in love with nature and imagination again. But I started to wonder—what if? It was just a fanciful dream, really. Not even a conjecture. But that's why I started studying. And why the games took so many years to finally make."

"So you could make the bridge," Brent pressed.

"Yes, precisely. Of course, we don't have the technology to actually go there. But we can interface with that world through the games."

A chill ran up my spine. I finally understood. The quantum physics equations. The research on alternate universes. With the insect pictures and the talk about an earthquake, I had thought this was about some kind of science research gone wrong. A bio weapon or an ecological disaster. But this wasn't about that at all. It wasn't even about Earth.

"Spatial manipulation," I said.

They were bending space and time to open a gateway to . . . somewhere else. Somewhere that you couldn't set foot, but you could "interface" with? What did that mean?

"How does the interface work?"

"Well, the precise technology is something I can't disclose. But basically, because the other worlds are digital, we can create an avatar in those worlds. You can travel around and go on adventures and make friends. Collect and trade and grow stronger as a team. That's what we wanted for children to experience."

Now I was confused again.

"But we didn't realize the danger," Satoshi continued, "We didn't know how many organizations on both sides of the bridge would try to exploit the bridge technology for profit. Or as a weapon. Not to mention the powers of the creatures themselves. I think it's good that you are children—even though you certainly aren't ordinary children! It will be easier for you to blend in when you go there to stop this. Because of their culture, you see?"

"You're giving this technology to children?" I asked.

Satoshi frowned curiously, "Yes, of course. You didn't . . . you didn't know about the games?"

He and Satō shot each other a worried look. I didn't know what else to ask, so I finally just asked it.

"What games?"

A blanket of silence hung over the table. Finally, Satoshi nodded. Satō placed the silver briefcase on the table, and it opened with a hydraulic swish. There, nestled snugly in a soft, protective foam was a strange, handheld contraption with dish-shaped receivers, a viewing screen, and dozens of buttons and knobs.

Resting comfortably beneath the device were two, small, rectangular cartridges: one red, and one blue.


End file.
